A single nucleotide polymorphism in the sheep κ-casein coding region

2005 ◽  
Vol 72 (3) ◽  
pp. 317-321 ◽  
Author(s):  
Maria Feligini ◽  
Slavica Vlaco ◽  
Vlatka Cubric Curik ◽  
Pietro Parma ◽  
GianFranco Greppi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genomic Region ◽  
Reference Sequence ◽  
Mature Protein ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Conventional Pcr ◽  
Homozygous State ◽  
Single Nucleotide ◽  
Forward Primer

Genetic polymorphisms in CSN3 gene in Pag (Croatia), Sarda (Italy) and Pramenka (Serbia) sheep breeds were investigated. A single nucleotide polymorphism (SNP) was localized by sequence analysis (sequence submitted to GenBank under accession AY237637) relying on an original primer pair. Primers for sequencing (κ-casF and κ-casR) were designed on the available CSN3 sequences to amplify the genomic region encoding the major part of the mature protein (exon 4). An SNP was detected at position 237 of the sheep κ-casein mRNA (reference sequence: GenBank X51822), where a thymine was substituted for a cytosine. The SNP was typed by conventional PCR and SYBR Green I-based real-time PCR. C and T alleles were discriminated using a dedicated set of primers that consisted of one common forward primer (SNP-TC) and two reverse primers (SNP-T and SNP-C), the latter two differing in the 3′ end base and in the presence of a 12 bp poly-G tail in SNP-C. The SNP was found in both the heterozygous and the homozygous state in Sarda and Pramenka breeds, and in the heterozygous state only in the Pag breed. The observed allelic frequencies of the SNP were 0·12 in Pag, 0·27 in Sarda and 0·45 in Pramenka.

Analysis of porcine OSBPL5 gene allelic expression in skeletal muscle and association of a single-nucleotide polymorphism in the coding region with production traits

2019 ◽  
Vol 99 (4) ◽  
pp. 914-920
Author(s):  
Meng Wang ◽  
Deli Wei ◽  
Guiling Cao ◽  
Guiyu Zhu ◽  
Yunliang Jiang
Keyword(s):  
Skeletal Muscle ◽  
Single Nucleotide Polymorphism ◽  
Growth Regulation ◽  
Average Daily Gain ◽  
Allelic Expression ◽  
Production Traits ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Specific Expression ◽  
Single Nucleotide

Genes that exhibit allelic expression imbalance and imprinted genes play important roles in the survival of the embryo and postnatal growth regulation. In this study, the porcine oxysterol-binding protein-related 5 (OSBPL5) gene was examined, and the 2140G>A mutation (rs318687202) was found in its coding region by a comparison of Laiwu and Landrace pigs. By allele-specific expression analysis based on a specific single-nucleotide polymorphism (SNP), the imprinting status of OSBPL5 gene in skeletal muscle from both neonate and adult pigs was determined. The results showed that the OSBPL5 was paternally imprinted in skeletal muscle from adults but biallelically expressed with predominantly maternal imprinting in neonates. The distribution of the 2140G>A SNP in four pig populations was analyzed, which showed that GG genotype was dominant in Duroc and Dapulian populations, whereas the AG genotype was dominant in Junmu-1 and Laiwu populations. Pigs with the GG genotype had significantly larger litters and greater cannon bone circumferences but a lower average daily gain than pigs with the AA genotype. In conclusion, we determined the difference in the allelic expression of OSBPL5 between adult and neonate pigs and identified an SNP in its coding region that is associated with production traits.

scholarly journals Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Anna Janowicz ◽  
Fabrizio De Massis ◽  
Massimo Ancora ◽  
Cesare Cammà ◽  
Claudio Patavino ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Brucella Melitensis ◽  
Reference Sequence ◽  
Snp Analysis ◽  
Phylogenetic Distance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

scholarly journals THE EFFECT OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) IN GLIOBLASTOMA MULTIFORME

2021 ◽  
Author(s):  
Asmita Ghosh ◽  
Dattatreya Mukherjee ◽  
Parth Patel ◽  
Debraj Mukhopadhyay
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Glioblastoma Multiforme ◽  
Association Studies ◽  
Disease Onset ◽  
Genetic Alterations ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Single nucleotide polymorphism is a genetic substitution of a base pair at a single position of the genome. SNPs are a common phenomenon and influence mRNA expression. Half of the SNPs occur in the non-coding region with 25% being mis-sense mutation and 25% being silent mutations. SNPs belong to the last generation of molecular markers which is identified through SNP mapping. SNPs are extensively studied to distinguish genetic expression and protein synthesis. These genetic differences are a major source of diseases in humans like cancers. One of the most common types of cancer of the brain is the Glioblastoma Multiforme that accounts for more than 80% of the malignant primary brain tumors (PBT). Researchers have found out a potential role of various SNPs in the genome to have a strong relation with Glioma formation and proliferation. Most SNPs are either not discovered, or their biological mechanisms are unknown, making it difficult to link putative associations with disease onset. The given review aims to identify some of the most common SNPs associated with GBM and classify the genetic basis along with future prospects. These SNPs are pioneer in Genome Wide Association studies to help in cancer research and identification of specific genetic alterations liked to GBM. Single Nucleotide Polymorphisms in a gene can be used as genetic biomarkers to aid better understanding of the mechanism of cancer formation, its aetiology, progression and metastatic behaviour.

Association Between Single-Nucleotide Polymorphisms of NKX2.5 and Congenital Heart Disease in Chinese Population: A Meta-Analysis

2021 ◽  
Author(s):  
Huan Chen ◽  
Tianjiao Li ◽  
Yuqing Wu ◽  
Xi Wang ◽  
Mingyuan Wang ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Single Nucleotide Polymorphism ◽  
Heart Disease ◽  
Chinese Population ◽  
Congenital Heart ◽  
Meta Analysis ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
China National Knowledge Infrastructure ◽  
Single Nucleotide

Abstract Background: NKX2.5 is a transcription factor that plays a key role in cardiovascular growth and development. Many independent studies have been conducted to investigate the association between the single nucleotide polymorphism 606G>C (rs3729753) in the coding region of NKX2.5 and congenital heart disease (CHD), although the results were inconsistent. This study aimed to reveal as much as possible the relationship between NKX2.5 single nucleotide polymorphism 606G>C and the risk of congenital heart disease in the Chinese population through meta-analysis.Methods and Results: After retrieving related articles in PubMed, MEDLINE, EMBASE, Web of science, Coherane, China National Knowledge Infrastructure (CNKI), Wanfang DATA, VIP database until Aug 2021, a total of 8 studies were finally included. Then, we merged the qualified research data into allele model, dominant model, recessive model, heterozygous model, homozygous model, additive model respectively. Overall meta-analysis results showed that 606G>C was not associated with congenital heart disease of the Chinese population in any model. Also, subgroup analysis based on congenital heart disease type gave the same negative result. Sensitivity analysis showed that there was no significant correlation after the deletion of each study. The results were negative and the heterogeneity was not significant.Conclusion: Our results show that NKX2-5 single nucleotide polymorphism 606G> C may not lead to the risk of congenital heart disease in Chinese.

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